﻿using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using NAligner;
using NAligner.formats;

namespace SmithWatermanTest
{
    class Program
    {
        static void Main(string[] args)
        {
             Sequence s1 = new Sequence();
             s1.AAList = "*DDU";
                Sequence s2 = new Sequence();
                
                s2.AAList = "*DU";
                float[,] scoreMatrix=new float[,]{{1,2},{2,3}};
                Matrix m = new Matrix("mm", scoreMatrix);

                Alignment alignment = SmithWatermanGotoh.Align(s1, s2, m, 0f, 0f);

                
                Console.WriteLine(new Pair().Format(alignment));
        }
    }
}
